Sequence
atgc intronic sequence ATGC exonic sequence...aattgaattcttctcatcatcagcagtgttgcagagtgtgaagtggtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
Basic information
species | Physcomitrella patens |
transcript | PP1S79_180V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------aattgaattcttctcatc----atcagcagtgttgcagagtgtgaagtg-gtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
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gtactaattgttttgtgttctgattcaatgttcatttgtttctgattgcggacaaattgttgatttccttgcctgcgagattagatttgtcggaaactaagccttgtgtgaatgtttagctttctagatacttaatttaacgtgtt-atttttttttatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTACATCCAACAGAGCCATG
upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------aattgaattcttctcatcatcagcagtgttgcagagtgtg--aagtggtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatt--tcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
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gtactaattgttttttgttctgattcaatgtttatttgtttttggttgccgacaaattgttgatttcgttacctgcgagattagatttgtcggaaactaagcctagtgtgaatgttttgctttctggctacttaatctaac-gtgttattttgatttttgatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATG
upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------aattgaattcttctcatcatcagcagtgttgcagagtgtgaagtggtga--ttttatgcctgcacag-gttttgtgctgata-gtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
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gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgtttgattagcttttcagcgaccttttat-gtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 2
-aattgaattcttctcatcatcagcagtgttgcagagtgtgaagtggtgattttatgcctgcacaggttt---tgtgctgatagtgct-----gattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
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gtattgtttcgatttccat-ttagtttttttgagggatttctttttatgtcattcgctctgtttttttttcgctgtgttgataatttctttgcgttgtttttggttcagAGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATG
upper sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 2
-----------------aattgaatt--cttctcatcatcagcagtgttgcagagtgtgaagtggtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
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gtacgcttgtttattccctttgaattgatttctatgtacagattagatctcgatttgtttaatgtttaatagttgaa-gtattgatgtcattttgcttctggtaaattttggat--cagAGGAAACTCGCGCAAAGATCAGAGAGAGTAAAATCTGTGGATCTGCATCCATCTGAGCCATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|18345941|gb|BJ177984.1|BJ177984EST: CATGCCTCTTCGCTTAGCGATCAAG CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
genomic: CATGCCTCTTCGCTTAGCGATCAAGgtatgattca ... cttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
EST:
gi|18374691|gb|BJ206269.1|BJ206269EST: CATGCCTCTTCGCTTAGCGATCAAG CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
genomic: CATGCCTCTTCGCTTAGCGATCAAGgtatgattca ... cttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
EST:
gi|18366204|gb|BJ198282.1|BJ198282EST: CATGCCTCTTCGCTTAGCGATCAAG CGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
genomic: CATGCCTCTTCGCTTAGCGATCAAGgtatgattca ... cttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
21 (upstream exon),
22 (downstream exon)
Score:
3CCTCTTCGCTTAGCGATCAAGgtatgattca ... cttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG
tgctgat putative branch site (score: 3)
ttttcttatttc CT-rich tract
tgattttcttattt TA-rich tract